This preliminary report details the results of looking for pathway enrichment in each of the groups of genes produced by hierarchical clustering of the drug perturbations. I’ve cut the the data into 15, but this value can be changed if we decide on a different value. Otherwise, this analysis focuses on enriched pathways in the MSigDB database. Specifically, this analysis uses the Hallmark segment from: https://www.gsea-msigdb.org/gsea/msigdb.

As for this report, the panel on the left is sorted by the number of dark kinases in the cluster and displays both the number of pathway hits and dark kinases in the cluster. The number of each cluster is arbitrary. The entry for each cluster displays the kinases associated with the cluster along with the number of non-kinases genes. Below this table are the pathways that passed the enrichment analysis at the 0.01 false discovery rate level. I also corrected for running this analysis for all 15 clusters.

Overall Enrichment Stats

Overall, 47 pathways are enriched in at least one of the following clusters. Of these pathways 4 are only hit once. The following pathways are seen in two or more clusters:

Num: 4 (Pathways: 16 DK: 27)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (27) CAMKK1, CDK11A, CDK12, CDK17, CDKL1, CLK3, COQ8A, CSNK1G1, CSNK2A2, DYRK2, HIPK1, MAST2, NEK1, NEK4, NEK7, PAN3, PDIK1L, PHKG2, PIP5K1A, RIOK3, SCYL1, STK19, TAOK1, TESK1, TLK1, TLK2, ULK4
Light Kinase (61) ABL2, ADPGK, ARAF, ATM, AURKB, BAZ1A, BAZ1B, BRD4, BTK, BUB1, CAMK2A, CAMK2G, CDK1, CDK2, CDK3, CHEK1, CLK1, CSK, DDR2, DGKE, DGKZ, FER, GRK2, GRK7, GSK3A, GTF2F1, HKDC1, HSPB8, IRAK3, LYN, MAP2K7, MAP3K6, MAP4K4, MAPK6, MAPK7, MAPK8, MASTL, MELK, MLKL, MYLK2, NEK2, PAK1, PAK2, PASK, PI4KB, PIK3C3, PLK4, RPS6KA5, SIK1, SIK1B, SLK, SMG1, SRPK1, STK10, STK35, STK4, TPTEP2-CSNK1E, TTN, TYRO3, WEE1, YES1
Non-kinase Count 2741
label pval fdr signature geneset overlap hits
HALLMARK_G2M_CHECKPOINT 0.0e+00 0.0e+00 2829 200 79 AMD1,ATRX,AURKB,BRCA2,BUB1,CASP8AP2,CCNA2,CCNB2,CCNT1,CDC25A,CDC27,CDC6,CDK1,CENPA,CHEK1,CHMP1A,CTCF,CUL1,CUL3,CUL4A,CUL5,DKC1,DR1,E2F1,E2F2,E2F3,ESPL1,EWSR1,GINS2,GSPT1,HMGN2,HMMR,HNRNPD,HNRNPU,HSPA8,ILF3,INCENP,KIF2C,KIF5B,KMT5A,KPNA2,KPNB1,LMNB1,MCM3,NASP,NEK2,NSD2,NUP50,NUSAP1,ODF2,ORC6,PDS5B,PLK4,PML,POLE,PRC1,RACGAP1,RAD21,RAD54L,RBL1,RBM14,RPA2,RPS6KA5,SFPQ,SMARCC1,SMC2,SMC4,SRSF2,SS18,STAG1,TENT4A,TMPO,TNPO2,TOP2A,TPX2,TRA2B,TRAIP,TROAP,UBE2C
HALLMARK_E2F_TARGETS 0.0e+00 0.0e+00 2829 200 75 ANP32E,ATAD2,AURKB,BRCA2,BRMS1L,CCNB2,CDC25A,CDK1,CENPM,CHEK1,CNOT9,CTCF,CTPS1,DCK,DEK,DEPDC1,DIAPH3,ESPL1,GINS4,GSPT1,HMGB2,HMMR,HNRNPD,ILF3,ING3,IPO7,KIF2C,KPNA2,LMNB1,LUC7L3,MCM3,MCM4,MCM7,MELK,MMS22L,MSH2,NAP1L1,NASP,NUDT21,NUP153,NUP205,ORC6,PCNA,PDS5B,PHF5A,PLK4,POLD3,POLE,POP7,PSMC3IP,RACGAP1,RAD1,RAD21,RAD51AP1,RAN,RFC1,RNASEH2A,RPA2,SLBP,SMC3,SMC4,SNRPB,SPC24,SRSF2,STAG1,TCF19,TMPO,TOP2A,TRA2B,TUBB,UBE2T,UBR7,UNG,USP1,WEE1
HALLMARK_MYC_TARGETS_V1 0.0e+00 0.0e+00 2829 200 53 CCNA2,CDK2,COX5A,CTPS1,CUL1,CYC1,DEK,EEF1B2,EIF4A1,EIF4G2,GSPT1,HNRNPA1,HNRNPA2B1,HNRNPA3,HNRNPD,HNRNPU,IFRD1,KPNA2,KPNB1,MCM4,MCM7,MRPL9,NAP1L1,PABPC1,PCNA,PHB2,PSMA1,PSMA2,PSMA7,PSMB2,PSMC4,PSMC6,PSMD1,PSMD8,PWP1,RAN,RNPS1,RPL22,RRM1,RRP9,SET,SLC25A3,SMARCC1,SNRPA,SNRPA1,SRPK1,SRSF2,TRA2B,UBA2,USP1,VBP1,VDAC1,VDAC3
HALLMARK_MITOTIC_SPINDLE 0.0e+00 0.0e+00 2829 199 49 ALMS1,ARFGEF1,ATG4B,BIN1,BRCA2,BUB1,CCNB2,CDC27,CDK1,CDK5RAP2,CEP57,CEP72,CKAP5,CLIP1,CNTRL,CNTROB,CTTN,DOCK2,EPB41L2,ESPL1,HOOK3,INCENP,KIF1B,KIF2C,KIF5B,LMNB1,NEK2,NF1,NUSAP1,PCGF5,PCM1,PCNT,PPP4R2,PRC1,RAB3GAP1,RACGAP1,RALBP1,RASA2,RFC1,RICTOR,SMC3,SMC4,STAU1,TLK1,TOP2A,TPX2,TSC1,WASF1,WASF2
HALLMARK_PROTEIN_SECRETION 0.0e+00 0.0e+00 2829 96 28 ABCA1,ANP32E,AP1G1,AP2B1,AP3B1,ARCN1,ARFGEF1,ARFGEF2,ATP6V1H,CLTA,CLTC,DNM1L,ERGIC3,GALC,GLA,KIF1B,PPT1,RAB14,RER1,SCAMP3,SOD1,STAM,STX16,TMED2,VAMP3,VAMP7,VPS45,VPS4B
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0e+00 0.0e+00 2829 200 41 ABCB7,ACO2,ATP5F1B,ATP5MG,ATP5PB,ATP6V1G1,ATP6V1H,CASP7,COX5A,CS,CYC1,ECI1,GLUD1,GRPEL1,HSD17B10,HSPA9,IDH3B,ISCA1,MFN2,MRPL15,MRPS15,MRPS30,MTRF1,NDUFA9,NDUFS3,NDUFS7,NDUFS8,PDHA1,PDHX,PHB2,SLC25A3,SLC25A5,SUCLG1,SUPV3L1,TIMM10,TIMM50,UQCRC2,UQCRH,VDAC1,VDAC2,VDAC3
HALLMARK_DNA_REPAIR 0.0e+00 0.0e+00 2829 150 34 ADRM1,ALYREF,ARL6IP1,BRF2,DCTN4,DDB1,DGCR8,ELL,ELOA,ERCC8,GTF2F1,GTF2H1,NT5C3A,NUDT21,PCNA,POLD3,POLL,POLR1D,POLR2A,POLR3C,POM121,RAD51,RAD52,RAE1,RPA2,SF3A3,SNAPC5,SRSF6,SUPT5H,TAF1C,TMED2,UPF3B,ZNF707,ZWINT
HALLMARK_MTORC1_SIGNALING 0.0e+00 0.0e+00 2829 200 36 ABCF2,ACACA,ACTR3,ATP2A2,BUB1,CDC25A,CYB5B,EEF1E1,GBE1,GLA,GMPS,GSR,GTF2H1,HSPA9,IFRD1,MCM4,NFKBIB,NFYC,NUP205,PPP1R15A,PSMA3,PSMB5,PSMC2,PSMC4,PSMC6,PSMD12,RAB1A,RIT1,RRP9,SEC11A,SLC7A11,SORD,SSR1,TMEM97,UBE2D3,UNG
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 0.0e+00 0.0e+00 2829 113 26 ATF4,BAG3,CNOT2,CNOT4,CNOT6,DCP1A,DCP2,DKC1,EDC4,EIF4A1,EXOSC10,EXOSC4,EXOSC5,EXOSC9,FUS,HSPA9,KHSRP,KIF5B,NFYB,PAIP1,RRP9,SEC11A,SLC30A5,SRPRB,SSR1,TATDN2
HALLMARK_PI3K_AKT_MTOR_SIGNALING 1.0e-07 4.0e-07 2829 105 22 ACACA,ACTR3,AKT1S1,ATF1,CAB39L,CDK1,CDK2,CLTC,E2F1,ECSIT,FGF22,GNGT1,GRK2,MAPK8,NFKBIB,PLCG1,PPP2R1B,PTPN11,RIT1,SFN,TRAF2,UBE2D3
HALLMARK_MYC_TARGETS_V2 6.0e-07 2.5e-06 2829 58 15 EXOSC5,GRWD1,MAP3K6,MCM4,NIP7,PES1,PLK4,PPAN,PPRC1,PUS1,RRP9,SORD,SUPV3L1,TMEM97,UNG
HALLMARK_HEME_METABOLISM 3.2e-06 1.4e-05 2829 200 29 ADIPOR1,CCDC28A,CDC27,CIR1,CROCCP2,DCUN1D1,E2F2,EZH1,FBXO7,FOXJ2,GAPVD1,GMPS,GYPA,ICAM4,ISCA1,MKRN1,MOCOS,NARF,NEK7,NUDT4,RANBP10,RBM5,RIOK3,SLC25A38,SLC4A1,SLC6A9,SLC7A11,SYNJ1,TFDP2
HALLMARK_SPERMATOGENESIS 7.3e-06 2.8e-05 2829 135 22 BUB1,CCNB2,CDK1,CLVS1,COIL,CSNK2A2,DMC1,IL12RB2,KIF2C,MAST2,MEP1B,MLLT10,NCAPH,NEK2,OAZ3,PARP2,PHKG2,PIAS2,SIRT1,TOPBP1,VDAC3,ZC3H14
HALLMARK_UV_RESPONSE_UP 3.0e-05 1.1e-04 2829 158 23 AGO2,AMD1,BID,CASP3,CDK2,CLTB,CYB5B,DNAJA1,DNAJB1,EIF5,GRPEL1,HNRNPU,KLHDC3,LYN,NXF1,PARP2,PPIF,PPP1R2,PPT1,PSMC3,SHOX2,SPR,TYRO3
HALLMARK_ADIPOGENESIS 1.8e-04 5.5e-04 2829 200 25 ABCA1,ACO2,ALDH2,ARAF,BAZ2A,CMPK1,CS,CYC1,ELMOD3,GBE1,GHITM,GRPEL1,HSPB8,LEP,MRPL15,NDUFS3,PEX14,PFKFB3,RIOK3,RREB1,SAMM50,SOD1,SUCLG1,UBC,UCK1
HALLMARK_P53_PATHWAY 1.8e-04 5.5e-04 2829 200 25 CCNK,CDKN2AIP,COQ8A,DNTTIP2,FBXW7,HINT1,IP6K2,KLF4,MDM2,MXD1,NOTCH1,NUDT15,PCNA,POM121,PPP1R15A,PRKAB1,RB1,RCHY1,RNF19B,SFN,SLC19A2,SLC3A2,SLC7A11,TRAF4,WWP1

Num: 11 (Pathways: 14 DK: 19)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (19) CAMK1D, CAMKV, CDKL3, DYRK1B, LMTK2, LMTK3, MAP3K15, MAPK15, MARK1, MKNK1, NEK5, PIK3C2B, PIP5K1B, SBK1, SCYL2, STK3, TESK2, TSSK1B, VRK3
Light Kinase (46) ACVR1C, ACVR2A, ACVRL1, ANKK1, BMP2K, BMX, CAMK2B, CAMK4, CDK9, CSF1R, DAPK1, DAPK2, DCLK1, EPHA6, EPHB2, EPHB3, FGFR1, FGFR2, FGFR3, FGFR4, FLT4, HCK, ITK, JAK2, KALRN, KSR1, KSR2, MAP2K3, MAP2K6, MAP4K1, MAPK10, MAPK11, MAST1, MATK, PI4KAP2, PRKCG, PRKCZ, PRKD2, PTK2, RPS6KA3, SGK2, SRPK2, STK26, STYK1, TAF1L, TXK
Non-kinase Count 1748
label pval fdr signature geneset overlap hits
HALLMARK_APICAL_JUNCTION 0.0e+00 0.0e+00 1813 200 31 ACTN2,ADAM23,AMIGO1,ATP1A3,CADM2,CALB2,CD209,CD34,CD86,CDH1,CDH15,CDH3,CNTN1,DHX16,DSC3,ICAM2,JAM3,KCNH2,LAYN,MAPK11,NECTIN2,NFASC,NRXN2,PARD6G,PPP2R2C,PTK2,SLC30A3,SYMPK,TJP1,TRO,VCAN
HALLMARK_SPERMATOGENESIS 0.0e+00 1.0e-07 1813 135 22 ACE,ALOX15,CAMK4,CHRM4,CNIH2,CRISP2,DCC,DDX25,DMRT1,GAD1,GSG1,GSTM3,JAM3,MAP7,MLF1,NOS1,SCG3,SEPTIN4,STAM2,STRBP,TNNI3,TUBA3C
HALLMARK_ALLOGRAFT_REJECTION 0.0e+00 1.0e-07 1813 200 27 ACHE,ACVR2A,CD1D,CD3D,CD40,CD74,CD86,CDKN2A,CRTAM,GPR65,IL11,IL12A,IL16,IL2RB,IL7,INHBB,ITGAL,ITK,JAK2,MAP4K1,NOS2,PRKCG,RPL3L,STAB1,STAT4,UBE2D1,WAS
HALLMARK_ESTROGEN_RESPONSE_LATE 0.0e+00 1.0e-07 1813 200 27 AFF1,ANXA9,CACNA2D2,CDH1,CYP26B1,DHRS2,DNAJC1,EMP2,FGFR3,IGSF1,JAK2,KCNK5,KLK10,KLK11,LSR,LTF,MOCS2,NPY1R,OLFM1,PDLIM3,PLAC1,PRKAR2B,S100A9,SLC1A4,SLC29A1,SULT2B1,TMPRSS3
HALLMARK_COMPLEMENT 0.0e+00 2.0e-07 1813 200 26 ACTN2,ATOX1,CLU,CPM,CR2,F5,FCN1,GCA,GRB2,HNF4A,HPCAL4,ITGAM,JAK2,KLK1,KLKB1,LGMN,LTF,MMP13,PIK3R5,PLA2G4A,PLAT,S100A9,SCG3,SH2B3,SPOCK2,WAS
HALLMARK_KRAS_SIGNALING_DN 1.0e-07 7.0e-07 1813 200 25 ABCG4,C5,CAMK1D,CLSTN3,CPEB3,CYP39A1,DCC,FGFR3,HSD11B2,IGFBP2,KCND1,KCNMB1,KCNN1,KLK7,NOS1,NR6A1,RYR1,SIDT1,SLC30A3,SLC5A5,SLC6A14,TAS2R4,TCF7L1,TFCP2L1,TNNI3
HALLMARK_IL2_STAT5_SIGNALING 1.1e-06 6.0e-06 1813 199 23 ABCB1,AHR,CD83,CD86,CST7,EOMES,ETFBKMT,FAM126B,GALM,GPR65,GUCY1B1,HUWE1,IL1R2,IL2RB,IL3RA,ITGA6,ITIH5,LRRC8C,MAP6,SELL,TLR7,TNFRSF8,TNFSF10
HALLMARK_ESTROGEN_RESPONSE_EARLY 1.2e-06 6.0e-06 1813 200 23 AFF1,ANXA9,CALB2,CYP26B1,DHRS2,ENDOD1,INHBB,JAK2,KAZN,KCNK5,KLK10,NPY1R,OLFM1,PDLIM3,PODXL,RAB17,REEP1,SLC1A4,SULT2B1,SYBU,TBC1D30,TMPRSS3,UGCG
HALLMARK_INFLAMMATORY_RESPONSE 1.2e-06 6.0e-06 1813 200 23 ACVR2A,ADGRE1,AHR,CCRL2,CD40,CD70,CYBB,FFAR2,IL2RB,LAMP3,NMUR1,NPFFR2,OPRK1,P2RX7,PIK3R5,PTAFR,PTGER4,SELL,SEMA4D,SLC28A2,STAB1,TNFSF10,TNFSF15
HALLMARK_MYOGENESIS 1.2e-06 6.0e-06 1813 200 23 ACHE,ACTN2,CAMK2B,CLU,CNN3,DAPK2,EIF4A2,EPHB3,FKBP1B,GNAO1,KCNH2,KLF5,MAPRE3,MYL2,NCAM1,NOS1,PTGIS,REEP1,RYR1,SLN,SPDEF,SPTAN1,TNNT2
HALLMARK_HEDGEHOG_SIGNALING 4.1e-06 1.9e-05 1813 36 9 ACHE,CRMP1,GLI1,HEY2,NKX6-1,NRP2,SCG2,SLIT1,TLE3
HALLMARK_INTERFERON_GAMMA_RESPONSE 1.4e-05 5.4e-05 1813 200 21 CD38,CD40,CD74,CD86,CIITA,IL2RB,IL7,ITGB7,JAK2,OASL,PELI1,PLA2G4A,SAMHD1,SLAMF7,ST3GAL5,STAT4,TDRD7,TNFSF10,TOR1B,TRAFD1,ZNFX1
HALLMARK_KRAS_SIGNALING_UP 1.4e-05 5.4e-05 1813 200 21 ABCB1,ACE,CBL,EPHB2,EVI5,FLT4,GPRC5B,GUCY1A1,IL33,KIF5C,MAP4K1,MAP7,MMD,PIGR,PLAT,SCG3,TMEM100,TMEM176B,TNNT2,TOR1AIP2,TPH1
HALLMARK_HEME_METABOLISM 4.5e-05 1.6e-04 1813 200 20 ACSL6,ADD2,ATG4A,BMP2K,BTRC,CDR2,ENDOD1,MAP2K3,MPP1,PSMD9,RAP1GAP,RBM38,RCL1,SLC30A10,SLC66A2,SPTA1,SPTB,TMCC2,TSPAN5,XK

Num: 10 (Pathways: 27 DK: 14)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (14) CDK19, DSTYK, HIPK3, LRRK1, MAP3K10, MARK4, NEK11, PIP4K2C, PIP5K1C, RPS6KC1, SBK3, SRPK3, STK38L, TTBK2
Light Kinase (32) AAK1, ABR, ACVR1, BRD2, CAMK2D, CSNK1D, DGKD, EIF2AK3, FRK, GSK3B, HK1, ILK, INSR, JAK1, LATS2, MAP2K2, MAP3K8, MAPK1, MAPKAPK2, MST1R, MYLK3, MYLK4, NRBP1, NUAK1, PEAK1, PI4K2A, PINK1, SIK3, TAOK3, TGFBR1, TRPM7, ULK1
Non-kinase Count 1183
label pval fdr signature geneset overlap hits
HALLMARK_CHOLESTEROL_HOMEOSTASIS 0.0e+00 0.0e+00 1229 74 20 ACAT2,ACSS2,ACTG1,CTNNB1,CYP51A1,EBP,ETHE1,FDFT1,FDPS,HMGCR,HMGCS1,IDI1,LGALS3,LSS,NSDHL,S100A11,SC5D,SCD,STARD4,TP53INP1
HALLMARK_MYOGENESIS 0.0e+00 0.0e+00 1229 200 27 ACSL1,APOD,APP,ATP6AP1,CHRNB1,COL6A2,DTNA,FDPS,FOXO4,GAA,GABARAPL2,HDAC5,ITGA7,ITGB1,LPIN1,MYL6B,MYO1C,NQO1,PC,PDE4DIP,PDLIM7,SCD,SIRT2,SORBS1,SVIL,TAGLN,TSC2
HALLMARK_MITOTIC_SPINDLE 0.0e+00 0.0e+00 1229 199 26 ABI1,ABR,AKAP13,ARHGAP10,ARHGAP5,ARHGEF12,ARL8A,CAPZB,CDC42,CDC42EP2,CSNK1D,CYTH2,DST,DYNC1H1,KIF3C,KIFAP3,MARK4,NEDD9,NOTCH2,OPHN1,PALLD,RABGAP1,RASAL2,SPTBN1,STK38L,WASL
HALLMARK_ANDROGEN_RESPONSE 0.0e+00 0.0e+00 1229 100 18 ABHD2,APPBP2,ARID5B,DHCR24,HMGCR,HMGCS1,IDI1,INSIG1,ITGAV,MYL12A,NCOA4,PLPP1,PTPN21,SCD,SLC38A2,TMEM50A,ZBTB10,ZMIZ1
HALLMARK_HEME_METABOLISM 0.0e+00 0.0e+00 1229 200 23 ALDH6A1,ARHGEF12,BLVRB,CLCN3,CTNS,CTSB,DMTN,FN3K,HTATIP2,KHNYN,LAMP2,LPIN2,LRP10,MBOAT2,MOSPD1,NCOA4,OPTN,PC,PGLS,PPP2R5B,SDCBP,SLC22A4,YPEL5
HALLMARK_FATTY_ACID_METABOLISM 0.0e+00 0.0e+00 1229 158 20 ACAT2,ACOT8,ACOX1,ACSL1,DECR1,DHCR24,EHHADH,ERP29,GLUL,HADHB,HMGCS1,HSD17B11,IDH1,IDI1,INMT,NSDHL,RETSAT,SERINC1,TP53INP2,VNN1
HALLMARK_APOPTOSIS 0.0e+00 0.0e+00 1229 161 20 APP,CTNNB1,CYLD,DCN,DNAJC3,EBP,HGF,HMOX1,IGF2R,IGFBP6,LGALS3,MADD,NEDD9,PPP2R5B,PSEN1,RETSAT,SC5D,SMAD7,SQSTM1,TIMP2
HALLMARK_IL2_STAT5_SIGNALING 0.0e+00 0.0e+00 1229 199 22 AHNAK,ANXA4,CAPG,CD81,CDC42SE2,COL6A1,CYFIP1,FURIN,IGF2R,ITGAV,KLF6,MAP3K8,MAPKAPK2,MYO1C,PLPP1,RABGAP1L,SERPINB6,SMPDL3A,SNX14,SNX9,SWAP70,TWSG1
HALLMARK_XENOBIOTIC_METABOLISM 0.0e+00 0.0e+00 1229 200 22 ACOX1,ADH5,AKR1C3,AQP9,BLVRB,CDA,DHRS7,HES6,HMOX1,HRG,HSD17B2,IDH1,LPIN2,NQO1,PC,PINK1,PMM1,PROS1,RETSAT,SLC12A4,UPB1,VNN1
HALLMARK_APICAL_JUNCTION 0.0e+00 1.0e-07 1229 200 21 ACTG1,ARHGEF6,BAIAP2,CAP1,CD276,CERCAM,CTNNA1,EXOC4,GNAI2,INSIG1,ITGB1,MADCAM1,MDK,MPZL1,MSN,MYL12B,RRAS,SGCE,SIRPA,THBS3,WASL
HALLMARK_BILE_ACID_METABOLISM 1.0e-07 5.0e-07 1229 112 15 ABCA9,ACSL1,AQP9,ATXN1,CYP8B1,DHCR24,HSD17B11,IDH1,IDI1,OPTN,PAOX,PEX6,PHYH,PRDX5,RETSAT
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 1.0e-07 6.0e-07 1229 200 20 CALD1,CAPG,COL6A2,DAB2,DCN,DST,FAP,FBLN5,FZD8,ITGAV,ITGB1,LAMC1,LRP1,MATN3,NOTCH2,PLOD2,PMP22,SGCB,TAGLN,VIM
HALLMARK_PEROXISOME 3.0e-07 1.1e-06 1229 104 14 ACOT8,ACOX1,ACSL1,ATXN1,CLN8,DHCR24,EHHADH,FDPS,HSD17B11,IDH1,IDI1,PEX6,PRDX5,RETSAT
HALLMARK_COMPLEMENT 6.0e-07 2.1e-06 1229 200 19 APOC1,C1S,CDA,CP,CPQ,CTSB,CTSD,FCER1G,GNAI2,GNB2,LAMP2,LGALS3,LRP1,PCSK9,PRCP,PSEN1,RHOG,S100A13,TIMP2
HALLMARK_MTORC1_SIGNALING 6.0e-07 2.1e-06 1229 200 19 ATP6V1D,CCNG1,CXCR4,CYP51A1,DHCR24,EBP,GSK3B,HMGCR,HMGCS1,IDH1,IDI1,INSIG1,PGM1,PLOD2,SC5D,SCD,SQSTM1,STARD4,TXNRD1
HALLMARK_TGF_BETA_SIGNALING 7.0e-07 2.2e-06 1229 54 10 ACVR1,CTNNB1,FURIN,NCOR2,RAB31,RHOA,SKIL,SMAD7,SPTBN1,TGFBR1
HALLMARK_UV_RESPONSE_DN 3.0e-06 8.7e-06 1229 144 15 ANXA4,ATP2B4,ATXN1,DAB2,FBLN5,INSIG1,LAMC1,MAP1B,NOTCH2,PMP22,PTPN21,SDC2,SMAD7,WDR37,ZMIZ1
HALLMARK_WNT_BETA_CATENIN_SIGNALING 7.3e-06 2.0e-05 1229 42 8 ADAM17,CTNNB1,FRAT1,FZD8,HDAC5,NCOR2,NUMB,WNT5B
HALLMARK_COAGULATION 8.5e-06 2.2e-05 1229 138 14 APOC1,C1S,CPQ,CTSB,FURIN,GNB2,HRG,LAMP2,LRP1,MST1,PROS1,S100A13,SIRT2,USP11
HALLMARK_HYPOXIA 1.1e-05 2.5e-05 1229 200 17 CAVIN3,CP,CXCR4,DCN,DTNA,EFNA1,FOSL2,GAA,HK1,HMOX1,KLF6,KLHL24,NAGK,PGM1,PRDX5,SDC2,SLC2A5
HALLMARK_OXIDATIVE_PHOSPHORYLATION 1.1e-05 2.5e-05 1229 200 17 ACAT1,ALDH6A1,ATP6AP1,ATP6V0E1,ATP6V1C1,ATP6V1D,ATP6V1E1,COX6A1,COX6C,CYB5R3,DECR1,HADHA,HADHB,IDH1,PHYH,RETSAT,RHOT1
HALLMARK_PROTEIN_SECRETION 2.5e-05 5.6e-05 1229 96 11 CD63,CLCN3,DST,GNAS,IGF2R,LAMP2,MAPK1,MON2,RAB9A,SNAP23,STX7
HALLMARK_ADIPOGENESIS 4.0e-05 8.0e-05 1229 200 16 ACOX1,APLP2,CD151,COX6A1,DECR1,DHRS7,ESYT1,IDH1,ITGA7,PGM1,PHYH,RETSAT,RNF11,SORBS1,SPARCL1,TANK
HALLMARK_ESTROGEN_RESPONSE_EARLY 4.0e-05 8.0e-05 1229 200 16 ABHD2,BLVRB,DYNLT3,FAM102A,FDFT1,FRK,KDM4B,MED13L,NCOR2,NRIP1,RAB31,SH3BP5,SLC37A1,SNX24,SVIL,TTC39A
HALLMARK_P53_PATHWAY 4.0e-05 8.0e-05 1229 200 16 APP,BAIAP2,CCNG1,CD81,CTSD,CTSF,EPS8L2,FGF13,HMOX1,MXD4,PHLDA3,PMM1,RALGDS,RETSAT,RPS27L,SERTAD3
HALLMARK_KRAS_SIGNALING_UP 1.4e-04 2.7e-04 1229 200 15 ADAM17,ADGRL4,APOD,CCSER2,CSF2RA,CXCR4,FCER1G,GALNT3,GPNMB,LY96,MTMR10,PTPRR,RABGAP1L,SPARCL1,ZNF277
HALLMARK_PI3K_AKT_MTOR_SIGNALING 2.7e-04 5.0e-04 1229 105 10 ADCY2,ARPC3,CXCR4,DUSP3,GSK3B,ITPR2,MAPK1,SQSTM1,STAT2,TSC2

Num: 5 (Pathways: 16 DK: 13)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (13) ALPK3, CDC42BPB, CDK15, CDKL5, ICK, NEK10, NEK8, NRBP2, PAK3, PAK6, STK32C, STK36, WNK3
Light Kinase (34) ABL1, AXL, CKB, DGKA, DGKB, DMPK, EIF2AK4, EPHA1, EPHA5, ERBB2, FGR, IGF1R, IKBKB, IKBKE, LIMK2, LRRK2, MAP2K5, MAP3K11, MAP3K12, MAPK3, MYLK, NPR1, PIK3CB, PKDCC, PRKCD, PRKD1, PRKY, RAF1, ROS1, STK16, STRADA, TIE1, TRIO, ULK2
Non-kinase Count 1605
label pval fdr signature geneset overlap hits
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.0e+00 0.0e+00 1652 200 35 ACTA2,ADAM12,ANPEP,BGN,BMP1,CADM1,CDH6,COL12A1,COL1A1,COL1A2,COL3A1,COL5A2,COL8A2,CXCL12,DKK1,EFEMP2,FBLN1,FBLN2,FSTL1,GAS1,LAMA3,MGP,MMP2,MYL9,MYLK,PCOLCE,PCOLCE2,PMEPA1,SNTB1,SPARC,TGFBI,TGFBR3,TPM1,TPM4,WNT5A
HALLMARK_ESTROGEN_RESPONSE_EARLY 0.0e+00 0.0e+00 1652 200 35 AKAP1,ALDH3B1,AR,ASB13,B4GALT1,CA12,CALCR,CCN5,CELSR1,CISH,CLDN7,CLIC3,CXCL12,ELOVL5,ESRP2,FKBP5,GFRA1,GREB1,IGF1R,KCNK15,MINDY1,MYOF,NAV2,OLFML3,OPN3,PDZK1,PEX11A,SEMA3B,SLC1A1,SLC22A5,SLC26A2,SLC27A2,SYT12,TMEM164,TSKU
HALLMARK_ADIPOGENESIS 0.0e+00 0.0e+00 1652 200 33 ACADL,ACADS,ACLY,ADCY6,ANGPT1,APOE,C3,CAVIN2,CD36,COL15A1,COQ9,CPT2,CYP4B1,DBT,DNAJC15,ETFB,GPAM,HADH,ITSN1,JAGN1,MARC2,MCCC1,MYLK,ORM1,PDCD4,PHLDB1,PPM1B,SCP2,SDHC,SLC25A1,SULT1A1,UCP2,VEGFB
HALLMARK_ESTROGEN_RESPONSE_LATE 0.0e+00 0.0e+00 1652 200 31 ALDH3B1,ASCL1,CA12,CALCR,CCN5,CISH,CKB,CLIC3,CPE,CXCL12,DLG5,ELOVL5,ETFB,FKBP5,GPER1,IMPA2,MYOF,OPN3,PDCD4,PDZK1,PLXNB1,SEMA3B,SERPINA3,SERPINA5,SLC22A5,SLC26A2,SLC27A2,SLC2A8,ST6GALNAC2,TNNC1,TRIM29
HALLMARK_MYOGENESIS 0.0e+00 0.0e+00 1652 200 28 ADAM12,AGL,AK1,ANKRD2,CASQ1,CAV3,CD36,CKB,COL15A1,COL1A1,COL3A1,DMPK,EFS,ENO3,ITGB4,LDB3,MB,MRAS,MYLK,MYOM1,NAV2,PLXNB2,PSEN2,PYGM,SPARC,TNNC1,TNNI2,VIPR1
HALLMARK_P53_PATHWAY 0.0e+00 0.0e+00 1652 200 28 ABHD4,ADA,AK1,ALOX15B,BLCAP,BTG2,CCND3,CDKN2B,CLCA2,DGKA,ERCC5,F2R,HEXIM1,ITGB4,PLXNB2,RXRA,SESN1,SLC35D1,STEAP3,TAX1BP3,TCHH,TCN2,TP53,TP63,TSPYL2,VAMP8,VDR,ZBTB16
HALLMARK_FATTY_ACID_METABOLISM 0.0e+00 0.0e+00 1652 158 24 ACADL,ACADS,ACOT2,ALDH3A1,ALDH9A1,AOC3,AQP7,AUH,CD36,CEL,CPOX,CPT2,ECI2,ELOVL5,ENO3,FMO1,GPD1,HADH,HPGD,MAOA,RDH11,SDHC,SLC22A5,SUCLG2
HALLMARK_APICAL_JUNCTION 0.0e+00 0.0e+00 1652 200 26 ACTG2,ACTN1,ACTN4,ALOX15B,B4GALT1,BMP1,CADM3,CDH6,CLDN7,CNN2,FSCN1,GNAI1,GRB7,HADH,INPPL1,ITGB4,LAMA3,LIMA1,MMP2,MYL9,NLGN3,PIK3CB,PIK3R3,PTPRC,TGFBI,VWF
HALLMARK_UV_RESPONSE_DN 0.0e+00 1.0e-07 1652 144 21 AGGF1,APBB2,ATRN,COL1A1,COL1A2,COL3A1,COL5A2,DMAC2L,EFEMP1,ERBB2,IGF1R,IGFBP5,MAP2K5,MIOS,NFIB,PIAS3,PIK3R3,RBPMS,RXRA,SMAD3,TGFBR3
HALLMARK_XENOBIOTIC_METABOLISM 0.0e+00 1.0e-07 1652 200 25 ABCC3,ALDH3A1,ALDH9A1,APOE,ATOH8,BCAR1,CD36,CFB,CRP,CYP17A1,CYP2C18,CYP2E1,DHRS1,ELOVL5,ENTPD5,FBLN1,FMO1,FMO3,IL1R1,MAOA,PPARD,PTGDS,SERPINA6,SLC35D1,SLC46A3
HALLMARK_BILE_ACID_METABOLISM 2.0e-07 8.0e-07 1652 112 17 ABCA4,ABCA8,ABCD1,ALDH9A1,AR,CYP7B1,HSD3B7,NUDT12,PEX11A,PEX11G,PEX13,PXMP2,RXRA,SCP2,SERPINA6,SLC27A2,SULT1B1
HALLMARK_PEROXISOME 3.0e-07 1.3e-06 1652 104 16 ABCD1,ALDH9A1,CADM1,CEL,ECI2,ELOVL5,HSD3B7,PEX11A,PEX11B,PEX13,RDH11,SCP2,SEMA3C,SERPINA6,SLC27A2,STS
HALLMARK_COMPLEMENT 3.5e-06 1.3e-05 1652 200 21 APOBEC3G,C1R,C3,CALM3,CD36,CFB,CR1,CTSH,CTSO,CTSS,DPP4,GATA3,GMFB,KCNIP3,MMP12,MSRB1,OLR1,PLSCR1,PRKCD,PRSS36,RAF1
HALLMARK_HEME_METABOLISM 1.2e-05 4.4e-05 1652 200 20 ACKR1,AGPAT4,ALDH1L1,BTG2,C3,CCND3,CPOX,ELL2,FBXO9,KAT2B,NFE2,NNT,PDZK1IP1,PIGQ,RHAG,SELENBP1,SIDT2,TAL1,TMEM9B,UCP2
HALLMARK_COAGULATION 5.6e-05 1.9e-04 1652 138 15 APOC3,BMP1,C1R,C3,CFB,CRIP2,CTSH,CTSO,DPP4,MMP2,MMP7,MSRB2,OLR1,SPARC,VWF
HALLMARK_APICAL_SURFACE 8.6e-05 2.7e-04 1652 44 8 ATP6V0A4,B4GALT1,EFNA5,FLOT2,GAS1,GATA3,PKHD1,RTN4RL1

Num: 2 (Pathways: 22 DK: 12)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (12) BRSK1, CDK11B, CDK16, CSNK1G3, MAP3K21, MARK3, PHKG1, RIOK1, RIOK2, RPS6KL1, STK40, VRK2
Light Kinase (35) AURKA, CASK, CDK4, CDK8, CSNK1A1, CSNK2A1, DGKG, EIF2AK2, EPHA2, FLT1, GAK, HK2, HUNK, IRAK2, MAP2K1, MAP3K4, MAPK9, MAPKAPK3, MAPKAPK5, MARK2, PAK4, PDPK2P, PIM1, PIM2, PLK2, PLK3, PRKAA1, RPS6KB1, SGK3, TAF1, TBK1, TEX14, TRIB2, TRIB3, TRIM33
Non-kinase Count 1556
label pval fdr signature geneset overlap hits
HALLMARK_MYC_TARGETS_V1 0.0e+00 0.0e+00 1603 200 68 ABCE1,ACP1,CANX,CBX3,CCT2,CCT3,CCT4,CCT5,CCT7,CDK4,CNBP,COPS5,DDX18,DDX21,EIF2S1,EIF2S2,EIF3D,EIF3J,EIF4H,EPRS1,ETF1,G3BP1,GLO1,GNL3,HSP90AB1,IARS1,ILF2,KARS1,MYC,NOLC1,NPM1,ODC1,PABPC4,POLD2,PRDX4,PSMA4,PSMA6,PSMB3,PSMD14,PSMD3,PSMD7,RACK1,RAD23B,RPL14,RPL18,RPL34,RPL6,RPLP0,RPS10,RPS2,RPS3,RPS5,RPS6,RSL1D1,RUVBL2,SF3A1,SNRPB2,SRSF1,SRSF3,SRSF7,TARDBP,TCP1,TUFM,U2AF1,XPO1,XPOT,XRCC6,YWHAE
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 0.0e+00 0.0e+00 1603 113 32 ALDH18A1,ASNS,ATF3,BANF1,CEBPG,CHAC1,CXXC1,DDX10,DNAJB9,EIF2S1,EIF4EBP1,EXOSC1,FKBP14,GOSR2,HERPUD1,IARS1,MTHFD2,MTREX,NFYA,NOLC1,NOP14,NPM1,PDIA6,PSAT1,RPS14,SDAD1,SERP1,SLC7A5,SRPRA,STC2,TARS1,XPOT
HALLMARK_MTORC1_SIGNALING 0.0e+00 0.0e+00 1603 200 40 ARPC5L,ASNS,AURKA,BCAT1,CANX,CCT6A,CFP,COPS5,CTH,DDIT3,DDX39A,EIF2S2,EPRS1,ETF1,GCLC,HK2,HSPA4,IMMT,M6PR,MTHFD2,NAMPT,NMT1,PHGDH,PNO1,PNP,PSAT1,PSMA4,PSMD13,PSMD14,PSMG1,RPN1,SERP1,SHMT2,SLC1A5,SLC7A5,TBK1,TCEA1,TFRC,TRIB3,UFM1
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0e+00 0.0e+00 1603 200 36 AREG,ATF3,BTG3,CCL20,CCL5,CD44,CXCL2,CXCL3,DUSP2,DUSP4,DUSP5,EIF1,FOSB,FOSL1,GADD45A,GFPT2,HBEGF,HES1,IER2,IER5,IFNGR2,IL15RA,IL23A,KLF10,MAFF,MCL1,MYC,NAMPT,PANX1,PHLDA1,PLK2,SLC16A6,SPHK1,TLR2,TNC,ZFP36
HALLMARK_MYC_TARGETS_V2 0.0e+00 0.0e+00 1603 58 17 BYSL,CBX3,CDK4,DDX18,DUSP2,GNL3,HK2,IMP4,MYC,NDUFAF4,NOLC1,NOP2,NPM1,RABEPK,RRP12,TFB2M,WDR43
HALLMARK_G2M_CHECKPOINT 0.0e+00 0.0e+00 1603 200 26 AURKA,CDK4,DDX39A,EZH2,G3BP1,H2BC12,HMGA1,HUS1,KATNA1,LIG3,MNAT1,MT2A,MYC,NOLC1,NUP98,ODC1,PAFAH1B1,PRIM2,PRMT5,RAD23B,SLC7A1,SLC7A5,SRSF1,UPF1,WRN,XPO1
HALLMARK_E2F_TARGETS 0.0e+00 2.0e-07 1603 200 24 AK2,ASF1A,AURKA,CDK4,DDX39A,EIF2S1,EZH2,HMGA1,HUS1,MTHFD2,MYC,NBN,NOLC1,POLD2,POLE4,PPM1D,PRDX4,PRIM2,SRSF1,TFRC,TIPIN,XPO1,XRCC6,ZW10
HALLMARK_P53_PATHWAY 0.0e+00 2.0e-07 1603 200 24 AEN,ATF3,DDIT3,EPHA2,FAS,GADD45A,HBEGF,IER5,MAPKAPK3,OSGIN1,PDGFA,PLK2,PLK3,PPM1D,RACK1,RAD9A,RPL18,RPL36,RPS12,SEC61A1,SERPINB5,SPHK1,TGFA,TRIB3
HALLMARK_UV_RESPONSE_UP 0.0e+00 2.0e-07 1603 158 21 ASNS,ATF3,BTG3,CDC34,CEBPG,CXCL2,DDX21,EIF2S3,FOSB,HSPA13,HTR7,MARK2,MSX1,NUP58,POLR2H,PRPF3,RAB27A,RPN1,TARS1,TFRC,TMBIM6
HALLMARK_ANDROGEN_RESPONSE 1.0e-07 6.0e-07 1603 100 16 ABCC4,ADAMTS1,CENPN,DNAJB9,ELK4,GNAI3,HOMER2,HSD17B14,LMAN1,NGLY1,PGM3,RRP12,SEC24D,SMS,UAP1,XRCC6
HALLMARK_ALLOGRAFT_REJECTION 2.2e-06 9.1e-06 1603 200 21 AARS1,ABCE1,BCAT1,BCL10,CCL5,CFP,DARS1,EIF3D,EIF3J,EREG,FAS,HLA-A,IFNGR2,IL4R,NPM1,RPL39,RPL9,RPS19,RPS3A,RPS9,TLR2
HALLMARK_INFLAMMATORY_RESPONSE 2.2e-06 9.1e-06 1603 200 21 ADORA2B,CCL20,CCL5,CD14,EIF2AK2,EREG,GNAI3,HBEGF,HRH1,IFNGR2,IL15RA,IL4R,IRAK2,MYC,NAMPT,SELENOS,SLC1A2,SLC31A1,SLC7A1,SPHK1,TLR2
HALLMARK_GLYCOLYSIS 7.9e-06 2.8e-05 1603 200 20 ADORA2B,AURKA,CD44,COPB2,CTH,ECD,GCLC,GFPT1,GMPPA,GNPDA1,HAX1,HK2,PFKP,PGAM1,PMM2,QSOX1,SLC35A3,STC2,TGFA,TXN
HALLMARK_KRAS_SIGNALING_UP 7.9e-06 2.8e-05 1603 200 20 BPGM,CCL20,CD37,DNMBP,DUSP6,EMP1,EREG,ETV4,ETV5,GFPT2,HBEGF,MALL,PLEK2,PRELID3B,PTBP2,SNAP25,SPRY2,TRIB2,USP12,WDR33
HALLMARK_APOPTOSIS 1.8e-05 6.1e-05 1603 161 17 ANXA1,ATF3,BCL10,BTG3,CD14,CD44,CTH,DAP3,DDIT3,DFFA,EMP1,EREG,ETF1,FAS,GADD45A,MCL1,PMAIP1
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY 2.3e-05 7.1e-05 1603 49 9 GCLC,GCLM,GLRX2,PFKP,PRDX4,PRNP,SELENOS,SRXN1,TXN
HALLMARK_IL2_STAT5_SIGNALING 2.5e-05 7.4e-05 1603 199 19 BATF3,CD44,EMP1,ETV4,HK2,IL4R,MAFF,MYC,NOP2,ODC1,PHLDA1,PIM1,PNP,PRNP,PTRH2,SLC1A5,SPRED2,SPRY4,ST3GAL4
HALLMARK_INTERFERON_GAMMA_RESPONSE 2.7e-05 7.5e-05 1603 200 19 BPGM,CCL5,EIF2AK2,FAS,GBP6,HLA-A,IL15RA,IL18BP,IL4R,LAP3,MT2A,MTHFD2,NAMPT,NUP93,P2RY14,PFKP,PIM1,PNP,RAPGEF6
HALLMARK_ESTROGEN_RESPONSE_EARLY 8.8e-05 2.3e-04 1603 200 18 AREG,CANT1,CD44,FHL2,HES1,KLF10,MREG,MYC,NBL1,PMAIP1,RRP12,SIAH2,SLC16A1,SLC39A6,SLC7A5,STC2,TFAP2C,THSD4
HALLMARK_IL6_JAK_STAT3_SIGNALING 1.1e-04 2.7e-04 1603 87 11 CD14,CD44,CXCL3,FAS,HAX1,IFNGR2,IL15RA,IL4R,INHBE,PIM1,TLR2
HALLMARK_PROTEIN_SECRETION 2.6e-04 6.1e-04 1603 96 11 ARFGAP3,COPB1,COPB2,COPE,GOLGA4,GOSR2,LMAN1,M6PR,RAB2A,SEC24D,ZW10
HALLMARK_XENOBIOTIC_METABOLISM 2.7e-04 6.1e-04 1603 200 17 ACP1,AP4B1,BCAT1,EPHA2,FAS,GCLC,HACL1,KARS1,LEAP2,LONP1,MT2A,NMT1,PYCR1,SHMT2,SLC1A5,TMBIM6,TYR

Num: 1 (Pathways: 15 DK: 11)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (11) ADCK1, ADCK5, CDC42BPG, COQ8B, CSNK2A3, MAST3, NEK9, PRAG1, PRKACB, STK32A, TAOK2
Light Kinase (31) BCR, BRD3, CKMT1A, CKMT1B, DGKQ, EIF2AK1, EPHA7, EPHB6, ERBB3, ERBB4, KDR, LIMK1, MAP3K13, MAP3K5, MAP4K2, MINK1, PRKACA, PRKCA, PRKCH, PRKX, PTK2B, ROCK2, RPS6KA2, RPS6KA6, SGK1, STK11, STK38, TGFBR2, TNK2, TRIM66, UHMK1
Non-kinase Count 1458
label pval fdr signature geneset overlap hits
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0e+00 0.0e+00 1500 200 27 ACADSB,ATP5F1C,ATP5F1D,ATP5F1E,ATP5PD,COX7A2,COX7C,CYB5A,ETFDH,GPX4,IDH2,MAOB,MPC1,NDUFB1,NDUFB3,NDUFB5,OGDH,OXA1L,PDHB,SLC25A11,SLC25A12,SLC25A20,SURF1,TIMM8B,UQCR11,UQCRB,UQCRQ
HALLMARK_GLYCOLYSIS 0.0e+00 1.0e-07 1500 200 25 AGRN,ALDH7A1,ALG1,ARPP19,B3GALT6,B3GAT3,BPNT1,CHST12,CHST2,CLDN9,COG2,CYB5A,GALK1,GLCE,HOMER1,LHPP,NDST3,PKP2,PPIA,PYGB,SDC3,SLC16A3,SRD5A3,STC1,XYLT2
HALLMARK_ESTROGEN_RESPONSE_LATE 0.0e+00 7.0e-07 1500 200 23 ABCA3,AGR2,ALDH3A2,ARL3,CD9,CELSR2,DCXR,HR,IDH2,ITPK1,LLGL2,NAB2,PLAAT3,RPS6KA2,SCARB1,SCNN1A,SGK1,SLC9A3R1,SNX10,TIAM1,TPD52L1,TST,UNC13B
HALLMARK_ADIPOGENESIS 8.0e-07 7.7e-06 1500 200 21 ABCB8,ADIPOQ,CAVIN1,COL4A1,COQ5,CRAT,DGAT1,ELOVL6,FZD4,GPHN,GPX4,LIFR,LIPE,LPCAT3,LPL,REEP6,SCARB1,SLC66A3,TST,UQCR11,UQCRQ
HALLMARK_APICAL_JUNCTION 8.0e-07 7.7e-06 1500 200 21 CDH8,CLDN11,CLDN9,CRAT,EVL,IRS1,ITGA3,JUP,LDLRAP1,MAP4K2,MYH10,NRTN,PECAM1,PTEN,RSU1,SDC3,SKAP2,TAOK2,TMEM8B,VCL,YWHAH
HALLMARK_PEROXISOME 2.9e-06 2.1e-05 1500 104 14 ABCD2,ABCD3,CRAT,DLG4,GSTK1,HMGCL,IDH2,ITGB1BP1,MLYCD,MVP,PEX2,PEX5,SLC35B2,YWHAH
HALLMARK_HEME_METABOLISM 3.0e-06 2.1e-05 1500 200 20 ARL2BP,ATP6V0A1,EIF2AK1,EPOR,ERMAP,GDE1,H1-0,LMO2,MARCHF2,MINPP1,PPOX,RNF123,SEC14L1,SLC10A3,SLC2A1,SNCA,TENT5C,TRAK2,TRIM58,UROS
HALLMARK_BILE_ACID_METABOLISM 7.0e-06 4.4e-05 1500 112 14 ABCA3,ABCD2,ABCD3,AMACR,CROT,GSTK1,IDH2,LIPE,MLYCD,NR1H4,PEX1,PEX7,SLC22A18,SLC35B2
HALLMARK_P53_PATHWAY 1.1e-05 6.1e-05 1500 200 19 CDKN1A,DCXR,GM2A,H1-2,H2AJ,H2AW,IFI30,JAG2,PITPNC1,PRMT2,PTPN14,RAP2B,S100A4,TGFB1,TM7SF3,TPD52L1,XPC,ZMAT3,ZNF365
HALLMARK_COAGULATION 1.9e-05 9.3e-05 1500 138 15 CASP9,CD9,CFI,CSRP1,DUSP14,F2RL2,F8,FN1,GNG12,HTRA1,PECAM1,PREP,RABIF,SERPING1,TF
HALLMARK_UV_RESPONSE_DN 3.1e-05 1.4e-04 1500 144 15 ANXA2,BCKDHB,CDON,DBP,DDAH1,GJA1,ID1,IRS1,LPAR1,MT1E,PRKCA,PTEN,PTPRM,SLC22A18,TGFBR2
HALLMARK_ESTROGEN_RESPONSE_EARLY 3.8e-05 1.5e-04 1500 200 18 ABCA3,ABLIM1,ADCY1,ADCY9,ARL3,BCL11B,CELSR2,GJA1,HR,ITPK1,PLAAT3,RPS6KA2,SCARB1,SCNN1A,SLC2A1,SLC9A3R1,TIAM1,TPD52L1
HALLMARK_XENOBIOTIC_METABOLISM 3.8e-05 1.5e-04 1500 200 18 ABCD2,ACP2,ARPP19,BPHL,CROT,CSAD,CYB5A,DCXR,ENPEP,ESR1,ETFDH,G6PC,JUP,MAN1A1,MPP2,SERTAD1,SPINT2,TKFC
HALLMARK_FATTY_ACID_METABOLISM 9.0e-05 3.2e-04 1500 158 15 ALDH3A2,BCKDHB,BPHL,CRAT,ETFDH,GSTZ1,HMGCL,LGALS1,MLYCD,PDHB,PPARA,REEP6,UBE2L6,UROS,YWHAH
HALLMARK_DNA_REPAIR 1.8e-04 6.1e-04 1500 150 14 APRT,DAD1,ERCC2,ERCC4,GPX4,MPG,POLR2E,POLR3GL,RBX1,SUPT4H1,SURF1,TAF10,TSG101,XPC

Num: 9 (Pathways: 9 DK: 9)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (9) ALPK2, BRSK2, CDK18, CDKL2, LTK, MAP3K14, PXK, STK31, STK33
Light Kinase (19) ACVR1B, AKT3, BRDT, DAPK3, EPHA4, ERN1, FES, FYN, GRK5, LCK, MAK, MAP3K9, MAP4K5, MERTK, NPR2, PRKCE, PRKG1, TNK1, TNNI3K
Non-kinase Count 962
label pval fdr signature geneset overlap hits
HALLMARK_GLYCOLYSIS 0.0e+00 0.0e+00 990 200 22 ARTN,CAPN5,CHPF2,CHST1,CITED2,COL5A1,FUT8,G6PD,GOT1,HS2ST1,HSPA5,KDELR3,LHX9,ME2,MERTK,P4HA1,P4HA2,PAM,PGM2,SOX9,UGP2,VLDLR
HALLMARK_HYPOXIA 1.0e-07 3.0e-06 990 200 18 CITED2,COL5A1,EDN2,FOXO3,HSPA5,KDELR3,LOX,P4HA1,P4HA2,PAM,PGM2,PPARGC1A,STBD1,TMEM45A,TPST2,UGP2,VLDLR,XPNPEP1
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 6.0e-07 1.0e-05 990 200 17 APLP1,COL5A1,CXCL8,ECM2,FBN1,FLNA,FUCA1,ID2,IL15,LOX,LUM,MAGEE1,MATN2,NID2,OXTR,P3H1,RHOB
HALLMARK_ADIPOGENESIS 1.2e-05 1.6e-04 990 200 15 ACAA2,ARL4A,ECH1,ENPP2,EPHX2,FABP4,FAH,MGST3,PPP1R15B,PREB,SLC27A1,SSPN,STOM,TOB1,YWHAG
HALLMARK_ESTROGEN_RESPONSE_EARLY 5.1e-05 3.7e-04 990 200 14 ABAT,AQP3,FLNB,KRT8,LRIG1,MAPT,P2RY2,PRSS23,RETREG1,SYNGR1,TJP3,TOB1,TUBB2B,WFS1
HALLMARK_KRAS_SIGNALING_DN 5.1e-05 3.7e-04 990 200 14 BRDT,EDN2,KCNE2,LYPD3,MFSD6,MX1,MYOT,P2RY4,PDE6B,RYR2,SNN,TFF2,THNSL2,THRB
HALLMARK_P53_PATHWAY 5.1e-05 3.7e-04 990 200 14 ABAT,ACVR1B,BAK1,CGRRF1,EPHX1,FOXO3,FUCA1,PERP,PROCR,STOM,TNNI1,TOB1,TSC22D1,VWA5A
HALLMARK_UV_RESPONSE_UP 8.0e-05 5.0e-04 990 158 12 AQP3,ATP6V1F,BAK1,BSG,C4BPB,CREG1,EPHX1,NAT1,NPTXR,PLCL1,RHOB,YKT6
HALLMARK_COAGULATION 1.0e-04 5.7e-04 990 138 11 ADAM9,CAPN5,CTSK,FBN1,FYN,GSN,MMP11,MMP15,PLG,PRSS23,RAPGEF3

Num: 3 (Pathways: 11 DK: 8)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (8) ADCK2, CAMKK2, CDK13, CSNK1G2, MAST4, NEK6, SCYL3, TP53RK
Light Kinase (16) ALPK1, CLK2, EGFR, MTOR, NLK, PDGFRA, PDK4, PIK3CG, PKN1, PKN2, ROR1, RYK, STK24, STK39, TBRG4, TEK
Non-kinase Count 876
label pval fdr signature geneset overlap hits
HALLMARK_KRAS_SIGNALING_UP 0.0e+00 0.0e+00 900 200 20 ALDH1A3,BIRC3,BTBD3,CA2,ETV1,FBXO4,GNG11,ITGBL1,LAPTM5,LAT2,LIF,MPZL2,PDCD1LG2,PLAU,PRRX1,PSMB8,RELN,RGS16,SCG5,TMEM158
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0e+00 1.0e-07 900 200 19 AIFM1,ATP5F1A,ATP5MC1,ATP5MC2,ATP5ME,ATP5PO,COX17,COX8A,FH,ISCU,MDH2,MRPS11,MTX2,NDUFA7,NDUFB6,NDUFS1,NDUFV1,PDK4,UQCRFS1
HALLMARK_DNA_REPAIR 6.0e-07 1.1e-05 900 150 14 CCNO,COX17,DDB2,ERCC1,GSDME,IMPDH2,MRPL40,NCBP2,NELFB,NELFE,POLR2G,POLR2I,SAC3D1,TAF9
HALLMARK_INTERFERON_ALPHA_RESPONSE 1.0e-05 1.3e-04 900 97 10 BATF2,CASP1,CMTR1,IFI44L,IFITM1,IRF2,MVB12A,PSMB8,PSMB9,TAP1
HALLMARK_XENOBIOTIC_METABOLISM 1.8e-05 1.8e-04 900 200 14 AHCY,ASL,CA2,CES1,CNDP2,DHPS,GCH1,GSS,IGFBP4,NINJ1,PDK4,PEMT,PSMB10,XDH
HALLMARK_FATTY_ACID_METABOLISM 3.2e-05 2.6e-04 900 158 12 ACSL4,ACSL5,ADSL,ALDH1A1,CA2,CYP4A11,FH,GCDH,GRHPR,MDH2,MGLL,PTPRG
HALLMARK_BILE_ACID_METABOLISM 3.7e-05 2.6e-04 900 112 10 ABCA6,ACSL5,ALDH1A1,EFHC1,GNPAT,LONP2,NEDD4,NR3C2,PEX12,SLC27A5
HALLMARK_IL2_STAT5_SIGNALING 7.3e-05 3.5e-04 900 199 13 AHCY,CA2,CCR4,IKZF2,IL18R1,IL1RL1,LIF,MUC1,NCS1,PDCD2L,RGS16,SYNGR2,UCK2
HALLMARK_ADIPOGENESIS 7.7e-05 3.5e-04 900 200 13 AIFM1,ATP5PO,COQ3,COX8A,ESRRA,MDH2,MGLL,MRAP,MTCH2,PEMT,QDPR,RMDN3,SQOR
HALLMARK_INFLAMMATORY_RESPONSE 7.7e-05 3.5e-04 900 200 13 CD82,GCH1,HAS2,IFITM1,IL18R1,LIF,MARCO,MEFV,RGS16,SGMS2,SRI,TLR3,TPBG
HALLMARK_INTERFERON_GAMMA_RESPONSE 7.7e-05 3.5e-04 900 200 13 BATF2,CASP1,CMTR1,GCH1,IFI44L,IRF2,NLRC5,PSMB10,PSMB8,PSMB9,SRI,TAP1,VCAM1

Num: 13 (Pathways: 16 DK: 6)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (6) CDK20, CLK4, DYRK3, DYRK4, NEK3, NUAK2
Light Kinase (12) ACVR2B, AURKC, BMPR1B, BRAF, CDK7, CSNK1E, MAP3K20, PIM3, PTK6, RIPK2, TRIB1, TRPM6
Non-kinase Count 536
label pval fdr signature geneset overlap hits
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0e+00 0.0e+00 554 200 50 BHLHE40,BIRC2,BMP2,BTG1,CEBPB,CFLAR,CSF2,CXCL1,CXCL10,DDX58,DRAM1,ETS2,GADD45B,ICAM1,IFIH1,IFIT2,IL1A,IL1B,IL6,INHBA,IRF1,JAG1,KYNU,LAMB3,MSC,NFKB2,NFKBIA,NFKBIE,PER1,PHLDA2,PLAUR,PLEK,PNRC1,PTGS2,PTX3,RELB,RIPK2,SERPINB8,SOD2,SPSB1,STAT5A,TGIF1,TNFAIP2,TNFAIP3,TNFAIP8,TNIP1,TRAF1,TRIB1,VEGFA,ZC3H12A
HALLMARK_INTERFERON_GAMMA_RESPONSE 0.0e+00 0.0e+00 554 200 27 BTG1,CMPK2,CXCL10,DDX58,DHX58,GBP4,ICAM1,IDO1,IFIH1,IFIT1,IFIT2,IL6,IRF1,ISG15,NFKBIA,PARP12,PTGS2,RBCK1,RIPK2,RSAD2,SOCS1,SOD2,TNFAIP2,TNFAIP3,TXNIP,UPP1,WARS1
HALLMARK_KRAS_SIGNALING_UP 0.0e+00 0.0e+00 554 200 21 AVL9,BMP2,C3AR1,CSF2,CXCL10,ETS1,HDAC9,HSD11B1,IKZF1,IL1B,INHBA,NGF,PLAUR,PRDM1,PTGS2,RBM4,ST6GAL1,TNFAIP3,TRAF1,TRIB1,TSPAN1
HALLMARK_INTERFERON_ALPHA_RESPONSE 0.0e+00 0.0e+00 554 97 15 CMPK2,CXCL10,DHX58,GBP4,HLA-C,IFIH1,IFIT2,IRF1,ISG15,NUB1,PARP12,RIPK2,RSAD2,TXNIP,WARS1
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.0e+00 0.0e+00 554 200 18 CXCL1,FERMT2,FGF2,GADD45B,IL32,IL6,INHBA,LAMC2,MMP1,PDLIM4,PLAUR,PPIB,PTX3,SNAI2,TFPI2,TNFAIP3,TNFRSF12A,VEGFA
HALLMARK_INFLAMMATORY_RESPONSE 0.0e+00 0.0e+00 554 200 18 C3AR1,CSF3,CSF3R,CXCL10,GNA15,ICAM1,IL1A,IL1B,IL6,INHBA,IRF1,NFKBIA,NLRP3,PLAUR,RIPK2,RNF144B,SLC11A2,SLC7A2
HALLMARK_HYPOXIA 0.0e+00 1.0e-07 554 200 15 AMPD3,BHLHE40,BTG1,CCNG2,CDKN1B,DDIT4,ETS1,GCNT2,HOXB9,IL6,NR3C1,PLAUR,PNRC1,TNFAIP3,VEGFA
HALLMARK_APOPTOSIS 0.0e+00 2.0e-07 554 161 13 BMP2,CDKN1B,CFLAR,GADD45B,GNA15,IL1A,IL1B,IL6,IRF1,KRT18,SOD2,TNFRSF12A,TXNIP
HALLMARK_IL6_JAK_STAT3_SIGNALING 0.0e+00 3.0e-07 554 87 10 CSF2,CSF3R,CXCL1,CXCL10,IL1B,IL6,IRF1,LTBR,SOCS1,TNFRSF12A
HALLMARK_ALLOGRAFT_REJECTION 1.0e-07 3.0e-07 554 200 14 DYRK3,ELF4,ETS1,HCLS1,HDAC9,ICAM1,IL1B,IL6,INHBA,NCK1,NLRP3,RIPK2,SOCS1,WARS1
HALLMARK_IL2_STAT5_SIGNALING 2.7e-06 1.2e-05 554 199 12 BHLHE40,BMP2,CDCP1,CSF2,CXCL10,GADD45B,GBP4,GSTO1,NFKBIZ,SOCS1,TRAF1,XBP1
HALLMARK_P53_PATHWAY 2.8e-06 1.2e-05 554 200 12 BMP2,BTG1,CDH13,DDIT4,DRAM1,IL1A,KRT17,NUPR1,SOCS1,TXNIP,UPP1,ZFP36L1
HALLMARK_PROTEIN_SECRETION 1.2e-05 4.7e-05 554 96 8 ARF1,BET1,KRT18,OCRL,RAB5A,TMED10,TOM1L1,YIPF6
HALLMARK_COMPLEMENT 1.7e-05 5.9e-05 554 200 11 CDH13,CEBPB,CXCL1,IL6,IRF1,KYNU,L3MBTL4,PLAUR,PLEK,TFPI2,TNFAIP3
HALLMARK_CHOLESTEROL_HOMEOSTASIS 1.9e-05 6.2e-05 554 74 7 CPEB2,JAG1,PLAUR,PNRC1,PPARG,STX5,TNFRSF12A
HALLMARK_UNFOLDED_PROTEIN_RESPONSE 4.0e-05 1.2e-04 554 113 8 ATF6,CEBPB,DDIT4,HYOU1,IFIT1,PDIA5,VEGFA,XBP1

Num: 6 (Pathways: 17 DK: 5)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (5) CDK14, OBSCN, STK17A, STK17B, TSSK4
Light Kinase (17) AATK, BLVRA, GRK3, GRK4, MAP3K1, MAPK13, MET, MYO3B, NTRK3, OXSR1, PDK3, PIK3CD, PRKCI, RIPK4, SNRK, SYK, TNIK
Non-kinase Count 550
label pval fdr signature geneset overlap hits
HALLMARK_INFLAMMATORY_RESPONSE 0.0e+00 0.0e+00 572 200 19 BDKRB1,CCL22,CD55,CX3CL1,EBI3,IL10,IRF7,ITGB3,LCP2,LDLR,MET,NOD2,P2RX4,PTPRE,SERPINE1,TAPBP,TIMP1,TNFAIP6,TNFSF9
HALLMARK_TNFA_SIGNALING_VIA_NFKB 0.0e+00 0.0e+00 572 200 18 BCL2A1,BCL6,FOS,FUT4,IL6ST,IRS2,LDLR,NFIL3,NR4A3,PDLIM5,PTPRE,SAT1,SDC4,SERPINE1,SOCS3,TIPARP,TNFAIP6,TNFSF9
HALLMARK_HYPOXIA 0.0e+00 0.0e+00 572 200 17 AKAP12,ALDOC,ANGPTL4,ERRFI1,FOS,IRS2,ISG20,LARGE1,MAP3K1,MXI1,NFIL3,PDGFB,PDK3,SDC4,SERPINE1,TGM2,TIPARP
HALLMARK_CHOLESTEROL_HOMEOSTASIS 0.0e+00 0.0e+00 572 74 11 ALDOC,CXCL16,DHCR7,ERRFI1,HSD17B7,LDLR,MVD,MVK,NFIL3,PDK3,SQLE
HALLMARK_COMPLEMENT 0.0e+00 0.0e+00 572 200 16 CASP4,CBLB,CD55,CD59,CFH,DOCK4,DOCK9,IRF7,LCP2,LTA4H,PDGFB,PDP1,PHEX,SERPINE1,SIRT6,TIMP1
HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 0.0e+00 1.0e-07 572 200 15 CD59,EDIL3,ITGA2,ITGB3,ITGB5,MMP3,NT5E,SAT1,SDC4,SERPINE1,SERPINE2,SPP1,TGM2,TIMP1,VEGFC
HALLMARK_IL2_STAT5_SIGNALING 1.0e-07 5.0e-07 572 199 14 CCND2,DHRS3,FGL2,GLIPR2,IFNGR1,IL10,NFIL3,NT5E,P2RX4,SH3BGRL2,SHE,SLC29A2,SPP1,TGM2
HALLMARK_INTERFERON_GAMMA_RESPONSE 1.0e-07 5.0e-07 572 200 14 CASP4,CFH,FGL2,HLA-B,IRF5,IRF7,ISG20,LCP2,PTPN1,SOCS3,SP110,TAPBP,TNFAIP6,TRIM25
HALLMARK_KRAS_SIGNALING_UP 1.0e-07 5.0e-07 572 200 14 AKAP12,ALDH1A2,ANGPTL4,ANKH,CCND2,CFH,EPB41L3,GABRA3,ITGA2,ITGB2,MAP3K1,SPP1,TSPAN13,TSPAN7
HALLMARK_UV_RESPONSE_DN 1.0e-06 4.7e-06 572 144 11 ADD3,CACNA1A,ICA1,INPP4B,ITGB3,LDLR,MET,PDLIM5,PIK3CD,SERPINE1,SYNJ2
HALLMARK_ESTROGEN_RESPONSE_EARLY 3.9e-06 1.8e-05 572 200 12 ADD3,DEPTOR,DHCR7,DHRS3,FOS,GAB2,IL6ST,KRT15,MPPED2,PTGES,TGM2,TIPARP
HALLMARK_COAGULATION 3.3e-05 1.4e-04 572 138 9 CFH,ITGA2,ITGB3,LTA4H,MMP3,PDGFB,SERPINE1,SH2B2,TIMP1
HALLMARK_IL6_JAK_STAT3_SIGNALING 6.6e-05 2.5e-04 572 87 7 CRLF2,EBI3,IFNGR1,IL6ST,ITGB3,PTPN1,SOCS3
HALLMARK_ALLOGRAFT_REJECTION 1.1e-04 3.4e-04 572 200 10 CCL22,CCND2,CD28,IFNGR1,IL10,IRF7,ITGB2,LCP2,TAPBP,TIMP1
HALLMARK_APOPTOSIS 1.1e-04 3.4e-04 572 161 9 ANKH,CASP4,CCNA1,CCND2,IFNGR1,ISG20,SAT1,SLC20A1,TIMP1
HALLMARK_ESTROGEN_RESPONSE_LATE 1.1e-04 3.4e-04 572 200 10 ADD3,CCNA1,DHCR7,FOS,IL6ST,ISG20,LARGE1,MAPK13,PTGES,TSPAN13
HALLMARK_P53_PATHWAY 1.1e-04 3.4e-04 572 200 10 APAF1,CCND2,FOS,HDAC3,PTPRE,RHBDF2,RRAD,SAT1,TM4SF1,TNFSF9

Num: 15 (Pathways: 3 DK: 5)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (5) CDC42BPA, CDK10, POMK, PSKH1, TSSK6
Light Kinase (16) CAMK1, CDK6, CHEK2, DCLK2, FASTK, LATS1, MAPK12, MAPK14, MOK, PIK3R4, PRKG2, RPS6KA4, RPS6KB2, STK25, TYK2, WNK4
Non-kinase Count 575
label pval fdr signature geneset overlap hits
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0e+00 0.00000 596 200 18 AFG3L2,ATP5MC3,ATP5MF,BAX,COX15,COX7B,ECHS1,MRPL34,NDUFA2,NDUFA3,NDUFB2,NDUFB7,NDUFC1,NDUFS2,NDUFS6,PMPCA,SDHA,UQCR10
HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY 2.5e-05 0.00054 596 49 6 LSP1,MGST1,MSRA,NDUFS2,STK25,TXNRD2
HALLMARK_ADIPOGENESIS 3.2e-05 0.00054 596 200 11 AGPAT3,CDKN2C,COX7B,DDT,ECHS1,MIGA2,NDUFB7,PFKL,SLC25A10,SNCG,UQCR10

Num: 8 (Pathways: 10 DK: 4)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (4) EEF2K, PKMYT1, PRPF4B, RSKR
Light Kinase (23) AKT1, ATR, BUB1B, CDC7, CHUK, CIT, EPHA3, FASTKD1, FASTKD2, FASTKD3, FASTKD5, GRK6, HASPIN, MAP3K7, PBK, PI4K2B, PLK1, PRKDC, RPS6KA1, STRADB, TRIM28, TTK, VRK1
Non-kinase Count 1112
label pval fdr signature geneset overlap hits
HALLMARK_E2F_TARGETS 0.0e+00 0.0e+00 1139 200 84 ASF1B,BARD1,BIRC5,BRCA1,BUB1B,CCNE1,CCP110,CDC20,CDCA3,CDCA8,CDKN3,CENPE,CIT,CKS1B,CKS2,CSE1L,DCLRE1B,DCTPP1,DLGAP5,DNMT1,DONSON,DSCC1,DUT,E2F8,EED,EXOSC8,GINS1,GINS3,H2AX,H2AZ1,HELLS,JPT1,KIF18B,KIF22,KIF4A,LBR,LIG1,LYAR,MAD2L1,MCM2,MCM5,MCM6,MKI67,MLH1,MRE11,MXD3,MYBL2,NCAPD2,NME1,NOP56,NUP107,ORC2,PA2G4,PAICS,PLK1,PNN,POLA2,POLD1,PPP1R8,PRKDC,PRPS1,PSIP1,PTTG1,RAD51C,RANBP1,RFC2,RFC3,RPA1,RPA3,RRM2,SMC1A,SMC6,SPAG5,SPC25,SSRP1,STMN1,SUV39H1,SYNCRIP,TACC3,TIMELESS,TK1,TRIP13,TUBG1,UBE2S
HALLMARK_G2M_CHECKPOINT 0.0e+00 0.0e+00 1139 200 60 BARD1,BIRC5,BUB3,CCNF,CDC20,CDC45,CDC7,CDKN3,CENPE,CENPF,CHAF1A,CKS1B,CKS2,DBF4,DTYMK,E2F4,EXO1,FANCC,FBXO5,H2AX,H2AZ1,H2AZ2,HIRA,JPT1,KIF11,KIF15,KIF20B,KIF22,KIF23,KIF4A,KNL1,LBR,MAD2L1,MCM2,MCM5,MCM6,MKI67,MTF2,MYBL2,NCL,NDC80,ORC5,PBK,PLK1,POLA2,POLQ,PRPF4B,PTTG1,SMC1A,SNRPD1,SRSF10,STIL,STMN1,SUV39H1,SYNCRIP,TACC3,TFDP1,TOP1,TTK,UBE2S
HALLMARK_MYC_TARGETS_V1 0.0e+00 0.0e+00 1139 200 58 APEX1,BUB3,C1QBP,CAD,CDC20,CDC45,CLNS1A,CSTF2,DHX15,DUT,EIF1AX,EIF3B,EIF4E,ERH,FBL,GOT2,H2AZ1,HDAC2,HNRNPC,HNRNPR,HPRT1,HSPD1,HSPE1,LSM7,MAD2L1,MCM2,MCM5,MCM6,NCBP1,NDUFAB1,NME1,NOP16,NOP56,ORC2,PA2G4,PHB,POLE3,PPM1G,PRDX3,PRPS2,PTGES3,RANBP1,RFC4,SERBP1,SNRPD1,SNRPD3,SNRPG,SRM,SSB,SSBP1,STARD7,SYNCRIP,TFDP1,TOMM70,TRIM28,TXNL4A,TYMS,UBE2L3
HALLMARK_MYC_TARGETS_V2 0.0e+00 0.0e+00 1139 58 21 DCTPP1,HSPD1,HSPE1,IPO4,LAS1L,MCM5,MPHOSPH10,MRTO4,MYBBP1A,NOC4L,NOP16,NOP56,PA2G4,PHB,PLK1,PRMT3,SLC19A1,SRM,TCOF1,UTP20,WDR74
HALLMARK_DNA_REPAIR 0.0e+00 0.0e+00 1139 150 28 BOLA2,CLP1,CSTF3,DUT,FEN1,GTF2A2,GTF2H3,GTF3C5,HPRT1,LIG1,NME1,POLA1,POLA2,POLD1,POLR1C,POLR2D,POLR2F,POLR2K,PRIM1,RFC2,RFC3,RFC4,RFC5,RPA3,SNAPC4,SSRP1,TYMS,UMPS
HALLMARK_MITOTIC_SPINDLE 0.0e+00 0.0e+00 1139 199 30 ANLN,ARAP3,BIRC5,CENPE,CENPF,CENPJ,CEP192,DLGAP5,ECT2,FBXO5,GEMIN4,KIF11,KIF15,KIF20B,KIF22,KIF23,KIF4A,KNTC1,NDC80,PIF1,PLEKHG2,PLK1,RHOT2,SASS6,SHROOM2,SMC1A,TTK,TUBA4A,TUBGCP3,TUBGCP5
HALLMARK_MTORC1_SIGNALING 0.0e+00 0.0e+00 1139 200 24 ADIPOR2,CACYBP,CCNF,CTSC,DHFR,FDXR,HPRT1,HSPD1,HSPE1,MCM2,MTHFD2L,NUFIP1,PDAP1,PITPNB,PLK1,POLR3G,PSME3,PSPH,RPA1,RRM2,STIP1,TUBA4A,TUBG1,UCHL5
HALLMARK_OXIDATIVE_PHOSPHORYLATION 0.0e+00 0.0e+00 1139 200 22 ATP5PF,COX11,CYCS,DLAT,FXN,GOT2,IDH3A,LDHB,MRPL11,MRPL35,MRPS12,MRPS22,NDUFAB1,OPA1,POLR2F,PRDX3,RHOT2,SDHB,SDHD,TIMM17A,TOMM22,TOMM70
HALLMARK_UV_RESPONSE_UP 3.7e-06 2.1e-05 1139 158 15 AP2S1,CCNE1,CDC5L,CHRNA5,FEN1,FKBP4,H2AX,PDAP1,POLE3,POLG2,PPAT,RASGRP1,RFC4,STIP1,TUBA4A
HALLMARK_ADIPOGENESIS 6.2e-05 3.1e-04 1139 200 15 ADIPOR2,ATL2,ATP1B3,CHUK,CMBL,DHRS7B,DLAT,GPD2,IDH3A,NDUFAB1,PRDX3,PTCD3,SDHB,SLC19A1,SLC5A6

Num: 12 (Pathways: 0 DK: 4)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (4) BCKDK, PKN3, TBCK, TSSK3
Light Kinase (15) AKT2, BMPR1A, DDR1, DGKH, DGKI, HIPK2, IRAK1, MAP3K3, MAP4K3, PDPK1, PIK3CA, RIPK1, SIK2, TRRAP, WNK1
Non-kinase Count 394
label pval fdr signature geneset overlap hits

Num: 7 (Pathways: 5 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) MKNK2, NIM1K
Light Kinase (5) DYRK1A, MAP3K2, PDK1, PRKAA2, TEC
Non-kinase Count 390
label pval fdr signature geneset overlap hits
HALLMARK_HYPOXIA 0.0e+00 0.00000 397 200 33 AK4,ALDOA,ANKZF1,BNIP3L,DPYSL4,EFNA3,ENO1,ENO2,ERO1A,F3,FAM162A,GAPDH,GLRX,GPI,IDS,IGFBP3,KLF7,LDHA,NDRG1,PDK1,PGF,PGK1,PLIN2,PPFIA4,PPP1R3C,RBPJ,RRAGD,SAP30,SLC2A3,SLC6A6,TPD52,TPI1,WSB1
HALLMARK_GLYCOLYSIS 0.0e+00 0.00000 397 200 27 ABCB6,AK4,ALDOA,ANG,ANKZF1,DPYSL4,EFNA3,EGLN3,ENO1,ENO2,ERO1A,FAM162A,GLRX,GNE,IGFBP3,LDHA,ME1,NOL3,PGK1,PKM,PLOD1,PPFIA4,RRAGD,SAP30,SPAG4,TALDO1,TPI1
HALLMARK_MTORC1_SIGNALING 0.0e+00 0.00000 397 200 18 AK4,ALDOA,EGLN3,ENO1,ERO1A,FADS1,GAPDH,GLRX,GPI,LDHA,ME1,MLLT11,PDK1,PGK1,PRDX1,SLC2A3,SLC6A6,TPI1
HALLMARK_PROTEIN_SECRETION 1.2e-05 0.00015 397 96 7 AP2M1,AP3S1,BNIP3,GBF1,SCAMP1,SEC31A,TPD52
HALLMARK_OXIDATIVE_PHOSPHORYLATION 3.6e-05 0.00036 397 200 9 ACADVL,BCKDHA,COX6B1,ETFA,GPI,LDHA,NDUFA6,NDUFA8,POR

Num: 14 (Pathways: 1 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) PI4KA, RNASEL
Light Kinase (16) BMPR2, CDK5, EPHA10, EPHB4, FPGT-TNNI3K, JAK3, MAP2K4, PDGFRB, PDK2, PIK3C2A, PRKD3, PTK7, ROCK1, SPEG, SRC, TRIM24
Non-kinase Count 435
label pval fdr signature geneset overlap hits
HALLMARK_MITOTIC_SPINDLE 2.4e-06 0.00012 453 199 11 APC,ARHGEF11,CD2AP,CEP131,DLG1,DYNLL2,KIF3B,MID1,MYH9,ROCK1,TBCD